I'm trying to install bioperl the way you prescribed. I'm stuck on the step four, though. The command sudo goes on installing several things, till it hits the netpbm and fails with the following messages:
“Error: org.macports.fetch for port netpbm returned: Subversion check out failed
Error: Failed to install netpbm
Please see the log file for port netpbm for details:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_netpbm/netpbm/main.log
Error: The following dependencies were not installed: gts netpbm libLASi pango Xft2 xrender xorg-renderproto cairo libpixman xorg-xcb-util urw-fonts xorg-libXaw xorg-libXmu
To report a bug, follow the instructions in the guide:
http://guide.macports.org/#project.tickets
Error: Processing of port graphviz failed”
Could you help me on this, please? I had tried several other ways to install bioperl, with no success.
Thank you.

Well, MacPorts was unable to retrieve netpbm, so it erred out. Looking at the MacPorts issue site, this seems to be a recurring problem related to the availability of the subversion server that hosts netpbm.

The best place to ask for assistance/report the problem would probably be Ticket 32000.